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Rui Fu
RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus
My research interests are in the various aspects of post-transcriptional gene expression regulation, particularly RNA degradation. In lieu of 10 years of bench research experience, I have now worked 3 years in computational roles analyzing high throughput sequencing data.
Education
Ph.D. Biological Science
University of California San Diego
La Jolla, CA, USA
2015 - 2009
B.S. Biological Science
Xiamen University
Xiamen, Fujian, China
2009 - 2005
Research Experience
Bioinformatic tool development: 1) clustifyr, single cell RNA-seq cell identity assignment (author); 2) squirrelBox, RNA-seq data visualization, exploration, and analysis web browser built with R Shiny and JavaScript (author); 3) valr, tidyverse-style genomic interval analysis (co-developer); 4) scraps, extraction of polyadenylation site info from scRNA-seq data (co-developer)
Semi-Independent Informatics Fellow
Jay Hesselberth’s Supervision
University of Colorado Anschutz
Current - 2017
- Development of bioinformatics software packages
- RNA-seq analysis and transcriptome annotation improvements for hibernating ground squirrel brain
- Informatics collaboration on various RNA biology projects, analyzing genomic and sequencing data
Postdoctoral Research Fellow
Judy Lieberman’s Lab
Harvard Medical School
2017 - 2016
- Identification of the mitochondrial trigger of apoptotic mRNA decay
- Purification of cytotoxic granules and key cytolytic proteins
- Mouse genetic manipulation by CRISPR-Cas9, and automated genotyping with custom R app
Graduate Research Assistant
Jens Lykke-Andersen’s Lab
University of California San Diego
2015 - 2009
- Investigation of co-factors involved in ZFP36 (TTP)-mediated mRNA decay and translational repression during the immune response of macrophages
- Characterization of the roles of ZFP36 family proteins in cell cycle progression regulation of mouse embryonic fibroblasts
Undergraduate Research Assistant
Ruichuan Chen’s Lab
Xiamen University
2009 - 2007
- Exploration of cell cycle and apoptosis implications of the transcription elongation regulator HEXIM1
- Mechanistic characterization of p-TEFb activation by HIV-Tat
Teaching Experience
Additional pedagogy training through the Harvard Medical School Scientists Teaching Science Course
Developed computational biology course materials: 1) rnabioco.github.io/practical-data-analysis; 2) rnabioco.github.io/cellar
Online Lecture Instructor (Graduate Level Courses)
University of Colorado Anschutz
N/A
Current - 2020
- Teaching with RStudio Cloud for Informatics and Statistics for Molecular Biology
- Zoom lectures, paper discussion, and exam/homework design for RNA section of Foundations in Biomedical Sciences
Lecture Instructor (Graduate Level Courses)
University of Colorado Anschutz
N/A
Current - 2018
- Lecture for RNA sequencing section of Rigor in Research (2020)
- Lectures, paper discussion, and exam/homework design for RNA section of Foundations in Biomedical Sciences (2018, 2019)
- Course Development and Lectures for Practical Data Analysis with R/RStudio (2018, 2019)
- Course Development and Lectures for Workshop for scRNA-seq Data Analysis (2019)
Teaching Assistant (Graduate Level Courses)
University of Colorado Anschutz
N/A
Current - 2018
- Practical Computational Biology for Biologists: R
- Practical Computational Biology for Biologists: Python
- Paper discussion for Core Topics in Biomedical Sciences
RNA Bioscience Initiative Informatics Office Hour (weekly)
University of Colorado Anschutz
N/A
Current - 2017
- Guidance on RNA and computational research questions from students and researchers of CU Anschutz Medical Campus
RNA Bioscience Initiative Summer Internship Mentoring
University of Colorado Anschutz
N/A
2020
- Mentoring of undergraduate summer research, systemically exploring published scRNA-seq cell type signatures in the NCBI Gene Expression Omnibus
- Project, archived at github.com/rnabioco/scRNA-seq-Cell-Ref-Matrix, contributed to updates to R Bioconductor packages clustifyr and clustifyrdatahub
Summer Research Mentoring
Harvard Medical School
N/A
2017
- Mentoring of high school student enrolled in the MIT Research Science Institute program in tissue culture, RNA-related bench experiments, RNA-seq informatics analysis, and scientific writing
BS/MS Student Research Mentoring
University of California San Diego
N/A
2015 - 2013
- Mentoring of student research spanning undergraduate honor thesis and master thesis in biochemical investigations of RNA-binding protein functions
- Mentee was awarded Best Poster Presentation Award at 2014 UCSD Biological Sciences Annual Student Research Showcase
Teaching Assistant (Undergraduate Level Courses)
University of California San Diego
N/A
2012 - 2011
- Molecular Biology, DNA Recombination Lab x2
Posters and Talks
ClustifyR: automated single-cell RNA sequencing cluster classification
Keystone Symposia on Single Cell Biology (Poster)
N/A
2019
PNPT1 release from the mitochondrial intermembrane space triggers rapid decay of mRNA and poly(A)-tailed ncRNA during apoptosis
Boston Children’s Hospital PCMM Research Poster Session (Poster)
N/A
2017
PNPT1 release from the mitochondrial intermembrane space triggers rapid decay of mRNA during apoptosis
Boston Children’s Hospital PCMM Research Poster Session (Poster)
N/A
2016
TTP-mediated mRNA repression involves recruitment of the 4EHP-GYF2 complex
Cold Spring Harbor Laboratory mRNA Processing Meeting (Presentation)
N/A
2015
TTP represses translation of target mRNAs through the 4EHP-GYF2 complex
UCSD Mechanisms of Gene Expression Seminar (Presentation)
N/A
2014
TTP family proteins regulate the stability of retinoblastoma protein mRNAs during serum-stimulated G0-S transition
Cold Spring Harbor Laboratory mRNA Processing Meeting (Poster)
N/A
2013
The regulation of TTP family mRNA-decay factors during G0-S cell cycle progression
Keystone Symposia on Protein-RNA Interactions (Poster)
N/A
2012
Service, Training, Recognition
Society memberships: 1) RNA Society; 2) International Society for Computational Biology; 3) Genetics Society of America
RNA Bioscience Initiative Grant Review
N/A
N/A
Current - 2019
GENETICS Early Career Reviewer (Cellular Genetics section)
4 manuscripts reviewed for GENETICS and G3, tinyurl.com/rev-rf
N/A
Current - 2018
Peer review of manuscripts under Dr Lykke-Andersen, Dr Lieberman, Dr Hesselberth
N/A
N/A
Current - 2011
Admissions Committee Member for CU Graduate Experiences for Multicultural Students
N/A
N/A
2019
Mentor for CU Anschutz and Denver Campus ISCORE undergraduate mentorship program
N/A
N/A
2019
BioFrontiers Hackathon
N/A
N/A
2018
Data Incubator Data Science Fellowship
N/A
N/A
2017
Grant writing training under Dr Lieberman
N/A
N/A
2016
Harvard Medical School Scientists Teaching Science Course
N/A
N/A
2016
Organizer for UCSD Ethics Center’s Silent Spring (50th Anniversary) Project
N/A
N/A
2012
Dr Huang Memorial Scholarship, UC San Diego
N/A
N/A
2011 - 2009
National College Students Creativity Experiment Project
N/A
N/A
2009 - 2007
First-Class Scholarship
N/A
N/A
2008 - 2006
XMU University Merit Student
N/A
N/A
2008 - 2006
Science Outreach
~500 hours of weekend volunteering time logged
Facilitator at Denver Museum of Nature and Science - Prehistoric Journey section
N/A
N/A
Current - 2019
Visitor Education Volunteer at the New England Aquarium
N/A
N/A
2017 - 2016
Information Ambassador at the San Diego Zoo
N/A
N/A
2016 - 2015